Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014783.1 Corchorus olitorius cultivar O-4 contig14816, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41544
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4921 original size:18 final size:18
Alignment explanation
Indices: 4898--4932 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4888 ACAAAAATTG
4898 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
4916 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
4933 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:5086 original size:19 final size:19
Alignment explanation
Indices: 5062--5109 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
5052 TTTATAATTT
* *
5062 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
5081 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
5099 TTATATAATAA
1 TTAT-TAATAA
5110 ATGAACATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:5125 original size:23 final size:23
Alignment explanation
Indices: 5098--5141 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5088 TATATAAATA
*
5098 ATTA-TATAATAAATGAACATTCG
1 ATTATTAT-ATAAACGAACATTCG
5121 ATTATTATATAAACGAACATT
1 ATTATTATATAAACGAACATT
5142 TAAATGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATTATATAAACGAACATTCG
Found at i:5174 original size:35 final size:35
Alignment explanation
Indices: 5135--5210 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
5125 TTATATAAAC
*
5135 GAACATTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACATTTAAATGAACAATAAACGAGCCTGTTCGT
*
5170 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACATTTAAATGAACAATAAACGAGCCTGTTCGT
5205 GAACAT
1 GAACAT
5211 AAACGAACTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (35 bp):
GAACATTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:11402 original size:24 final size:26
Alignment explanation
Indices: 11370--11418 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
11360 AAAAATGCCC
*
11370 AAATTAC-AAATGAA-AAGAAAAAGG
1 AAATTACAAAATGAATAAAAAAAAGG
11394 AAATTACAAAATGAATAAAAAAAAG
1 AAATTACAAAATGAATAAAAAAAAG
11419 AATGCAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.14
Consensus pattern (26 bp):
AAATTACAAAATGAATAAAAAAAAGG
Found at i:12109 original size:20 final size:22
Alignment explanation
Indices: 12084--12124 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12074 TCAAGCTCAG
12084 CTCGAA-TTTTC-CGAGTCGAA
1 CTCGAATTTTTCTCGAGTCGAA
12104 CTCGAATTTTTCTCGAGTCGA
1 CTCGAATTTTTCTCGAGTCGA
12125 GCGCGAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
CTCGAATTTTTCTCGAGTCGAA
Found at i:18002 original size:33 final size:33
Alignment explanation
Indices: 17960--18027 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
17950 GGTTTACTTC
17960 GGTGTAATGGGATATACCCATGCAGTCGGAGAT
1 GGTGTAATGGGATATACCCATGCAGTCGGAGAT
17993 GGTGTAATGGGATATACCCATGCAGTCGGAGAT
1 GGTGTAATGGGATATACCCATGCAGTCGGAGAT
18026 GG
1 GG
18028 CCGGGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (33 bp):
GGTGTAATGGGATATACCCATGCAGTCGGAGAT
Found at i:33433 original size:1 final size:1
Alignment explanation
Indices: 33427--33489 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
33417 TGTAATGCTC
* * * * * * *
33427 TTTTTTTGTTTTCTTTTTTTGTTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33490 CCAAGATTGA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:33443 original size:13 final size:12
Alignment explanation
Indices: 33427--33489 Score: 87
Period size: 12 Copynumber: 5.4 Consensus size: 12
33417 TGTAATGCTC
33427 TTTTTTTGTTTT
1 TTTTTTTGTTTT
33439 CTTTTTTTG--TT
1 -TTTTTTTGTTTT
*
33450 TTGTTTTGTTTT
1 TTTTTTTGTTTT
33462 TTTTTTTG-TTT
1 TTTTTTTGTTTT
33473 TTTTTTTGTTTT
1 TTTTTTTGTTTT
33485 TTTTT
1 TTTTT
33490 CCAAGATTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
10 7 0.16
11 13 0.29
12 17 0.38
13 8 0.18
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:33456 original size:11 final size:11
Alignment explanation
Indices: 33427--33489 Score: 83
Period size: 11 Copynumber: 5.5 Consensus size: 11
33417 TGTAATGCTC
33427 TTTTTTTGTTT
1 TTTTTTTGTTT
33438 TCTTTTTT-TGTT
1 T-TTTTTTGT-TT
*
33450 TTGTTTTGTTTT
1 TTTTTTTG-TTT
33462 TTTTTTTGTTT
1 TTTTTTTGTTT
33473 TTTTTTTGTTT
1 TTTTTTTGTTT
33484 TTTTTT
1 TTTTTT
33490 CCAAGATTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
11 27 0.59
12 18 0.39
13 1 0.02
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:33456 original size:23 final size:23
Alignment explanation
Indices: 33430--33489 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
33420 AATGCTCTTT
33430 TTTTGTTTTCTTTTTTTG-TTTTG
1 TTTTGTTTT-TTTTTTTGTTTTTG
*
33453 TTTTGTTTTTTTTTTTGTTTTTT
1 TTTTGTTTTTTTTTTTGTTTTTG
33476 TTTTGTTTTTTTTT
1 TTTTGTTTTTTTTT
33490 CCAAGATTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 8 0.23
23 27 0.77
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (23 bp):
TTTTGTTTTTTTTTTTGTTTTTG
Done.